Export Scene to JSON that has Multiple Models that each have Multiple Materials
I personally would try one of these two things:


Bake an image for the whole object to be UV wrapped in, and then use that image as one material.


OR


Separate the Meshes per material, and export those out separately with their single materials. I know THREEJS anyway has groups that you could use to re-group all of the geometry, but I'm not sure that's what you are using JSON for.